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2018.02.16

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@tomka tomka released this 16 Feb 23:54
· 3995 commits to master since this release

2018.02.16

Contributors: Albert Cardona, Andrew Champion, Chris Barnes, Tom Kazimiers

Notes

  • Three new OS package dependencies have been added (due to a Django framework
    upgrade), make sure they are installed:

    sudo apt-get install binutils libproj-dev gdal-bin

  • Python 3.6 is now supported. Make sure to update your settings.py by replacing
    the line

    COOKIE_SUFFIX = hashlib.md5(CATMAID_URL).hexdigest()

    with the following line:

    COOKIE_SUFFIX = hashlib.md5(CATMAID_URL.encode('utf-8')).hexdigest()

  • A virtualenv upgrade is required. To correctly install one updated dependency,
    the django-rest-swagger Python package has to be removed first from from the
    virtualenv, before the virtualenv is updated:

    pip uninstall django-rest-swagger
    pip install -r requirements.txt

  • requirements files now inherit from each other: -test.txt includes
    the production requirements, -dev.txt includes test (and therefore
    production) and doc.

  • CATMAID extensions no longer require users to manually edit their
    INSTALLED_APPS in settings.py. Remove if they are already in use.

  • The NODE_PROVIDER settings variable (settings.py) is replaced with the
    NODE_PROVIDERS variable. The new variable takes a list of node provider names,
    which are iterated as long as no result nodes are found. Replace the former
    single string value with a list with this name as single element, e.g. if
    the current setting reads NODE_PROVIDER = 'postgis2d', replace it with
    NODE_PROVIDERS = ['postgis2d'].

  • Three new types of cache backed node providers have been added: cached_json,
    cached_json_text, cached_msgpack. Tests suggest that cached_msgpack is the
    fastest.

Features and enhancements

Reconstruction Sampler:

  • 3D previews now allow to use a white background and toggle meta spheres.

  • To match a given interval length, the Reconstruction Sampler will now create
    new nodes during interval creation. This allows better sampling on long
    straight lines without intermediate nodes. To disable this behavior uncheck
    the "Create bounding nodes" setting. Newly created nodes are automatically
    labeled with the "sampler-created" tag.

  • By adjusting the new interval "max error" setting, it is possible to only
    create bounding nodes (if enabled) if the closest existing node is farther
    away from the ideal location than the max error value. This allows better
    reuse of existing nodes.

  • Created interval boundary nodes are also automatically deleted on sampler
    removal, if possible. If a created node has not been altered in any way during
    its life time and it still forms a straight line with its parent and single
    child, it can be removed. Otherwise the node is kept.

  • A new "Partner" step has been added. After a connector is selected at random,
    users are now asked to add all partner nodes to the synapse and let the widget
    choose a partner site for them.

  • Sections that should be interpolated (e.g. because of large tracing data
    shifts due to image data shifts) are now respected and not over-sampled
    anymore.

  • Completed intervals can now be optionally excluded from random selection.

Node Search:

  • Tagged connector nodes are now shown in search results.

  • Annotation search results allow now to open the Neuron Navigator page for the
    respective annotation.

Graph Widget:

  • It is now possible to show links of all connector types. By default, only
    synaptic connectors are available, but this can be changed using the "Link
    types" drop down control in the Graph tab. There also the edge color for
    particular link types can be set.

  • The edge color button in the option dialog has been replaced with a link type
    drop down which allows to set color and visibility per connection type.

3D Viewer:

  • Stored interpolatable sections are now loaded by default. Additional project
    space sections can be configured from the Skeleton filters tab.

  • Custom tags can now also apply to predefined labels like TODO or
    uncertain_end.

Miscellaneous:

  • The maximum number of frames per second rendered by a stack viewer window can
    now be adjusted through the Settings Widget > Stack view > Max frames per
    second.

  • The Open Widget dialog is now only opened with Ctrl + Space when no other keys
    are pressed. This allows to use key combinations like Ctrl + Shift + Space + >
    to browse smoothly through the image stack while hiding the tracing layer.

  • The active node can now be moved in Z by holding the Alt key and
    using ,/.. The stack viewer follows the node.

  • Filters: a Reconstruction Sampler Domain node filer is now available. The
    required node ID can be optained from the Reconstruction Sampler Widget.

  • Neuron History: a lower and upper bound for the time window in which changes
    are respected and counted can now be set.

  • On CATMAID front-pages (project overview) the keys 0-9 can now be used to open
    the n-th stackgroup or stack, stackgroups have precedence.

  • Sections in which nodes should be interpolated for various displays can now be
    persisted in the database using the "interpolatable sections" data model from
    the admin interface.

Bug fixes

  • Reconstruction sampler: Strahler shading color updates work now reliably.

  • Reconstruction sampler: connectors in neighboring intervals are now not
    included anymore in connector listing.

  • 3D Viewer: SVG export styles are correctly applied again, the exported data
    isn't transparent anymore.

  • 3D Viewer: custom label matches are now always given precedence when multiple
    labels are matched on a node.